<tool id="vcfflatten2" name="VCFflatten:" version="0.0.3">
  <description>Removes multi-allelic sites by picking the most common alternate</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio" />
  <command>vcfflatten "${input1}" > "${out_file1}"</command>
  <inputs>
    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="vcfflatten-input1.vcf"/>
      <output name="out_file1" file="vcfflatten-test1.vcf"/>
    </test>
    </tests>
  <help>

Removes multi-allelic sites by picking the most common alternate.  Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype.

----

Vcfflatten @IS_PART_OF_VCFLIB@
</help>
  <expand macro="citations" />
</tool>